[BioC] weird problem with ReadAffy and makecdfenv'd CDF package
Tim
ttriche at usc.edu
Sat Feb 24 03:06:42 CET 2007
Sorry to bother the list with what is probably a dumb question.
I looked in the list archives and online, and in the code for the
routines ReadAffy and read.affybatch, and for the life of me, I
can't figure it out. I used library(makecdfenv) to create an
alternative CDF environment where I mask out some probes in a
probeset, and I try to load it into an affyBatch, and I get...
> library(PHYH)
> ReadAffy(verbose=TRUE,cdfname=PHYH)
1 reading /home/tim/Hacia/cb1.cel ...instantiating an AffyBatch
(intensity a 1354896x55 matrix)...done.
Reading in : /home/tim/Hacia/cb1.cel
Reading in : /home/tim/Hacia/cb2.cel
Reading in : /home/tim/Hacia/cb3.cel
...
Reading in : /home/tim/Hacia/ht6.cel
Error in as.character(args[[i]]) : cannot coerce to vector
>
Any suggestions? I can't figure out what's going on here. I have
loaded plenty of affyBatch'es of CEL files before, but never with an
alternatively masked CDF environment... when I do it like so,
> ReadAffy(verbose=TRUE)
1 reading /home/tim/Hacia/cb1.cel ...instantiating an AffyBatch
(intensity a 1354896x55 matrix)...done.
Reading in : /home/tim/Hacia/cb1.cel
Reading in : /home/tim/Hacia/cb2.cel
Reading in : /home/tim/Hacia/cb3.cel
...
* Installing *source* package 'hgu133plus2cdf' ...
** R
** data
** help
>>> Building/Updating help pages for package 'hgu133plus2cdf'
Formats: text html latex example
geometry text html latex example
hgu133plus2cdf text html latex
** building package indices ...
* DONE (hgu133plus2cdf)
The downloaded packages are in
/tmp/RtmpIMTi6e/downloaded_packages
Attaching package: 'hgu133plus2cdf'
The following object(s) are masked from package:PHYH :
i2xy
The following object(s) are masked from package:PHYH :
xy2i
AffyBatch object
size of arrays=1164x1164 features (582203 kb)
cdf=HG-U133_Plus_2 (54675 affyids)
number of samples=55
number of genes=54675
annotation=hgu133plus2
... it works OK. So should I unpack the hgu133plus2cdf package,
mask out probes (merge into a custom CDF), and then use that?
Seems like I am missing something obvious here. Need more eyes!
Much obliged, thank you in advance for your helpful advice,
--tim
--
"People seldom do what they believe in. They do what is convenient,
then repent."
--Bob Dylan
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